The overall goal of the Phase II project is to increase the information yield and reduce the labor of gene expression analysis by means of Multiplex Profiling (MP). MP is a third generation gene expression technology. To increase information, MP capitalizes on sequence signatures of protein coding DNA ("CodeSigs") to synthesize and identify transcripts differentially expressed in biological systems. To increase throughput, MP processes these samples by electrophoretic multiplexing and blotting onto nylon membranes. MP blots can then be queried by hybridization with a wide variety of probe configurations to profile gene expression. The multiplexing introduces tremendous latitude for gene transcript syntheses, while at the same time maintaining the capabilities for detection of individual transcripts in this set. We will generate a collection of 100 CodeSigs using modem informatics tools including computational analysis of sequence motifs in genes and from structural conservation of DNA sequences in critical protein domains. We will derive standard conditions for cDNA synthesis, amplification, probing and retrieval of differentially expressed transcripts with CodeSigs. PROPOSED COMMERCIAL APPLICATION: Multiplex profiling as designed in the Phase II plan represents a third generation system for profiling gene expression. The modular kit design will provide complete reagents for profiling gene expression by either domain or motif-directed cDNA synthesis, or random cDNA synthesis, allowing tremendous impact on gene discovery programs within both research and pharmaceutical platforms.